Related papers: Determining Free Energy Differences Through Variat…
The first-principles-based effective Hamiltonian scheme provides one of the most accurate modeling technique for large-scale structures, especially for ferroelectrics. However, the parameterization of the effective Hamiltonian is…
Quantitative evaluations of the free energy of materials must take into account thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
In the long-time pursuit of the solution to calculate the partition function (or free energy) of condensed matter, Monte-Carlo-based nested sampling should be the state-of-the-art method, and very recently, we established a direct integral…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
The classical Hamiltonian system of time-dependent harmonic oscillator driven by the arbitrary external time-dependent force is considered. Exact analytical solution of the corresponding equations of motion is constructed in the framework…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
Free energies govern the behavior of soft and liquid matter, and improving their predictions could have a large impact on the development of drugs, electrolytes or homogeneous catalysts. Unfortunately, it is challenging to devise an…
Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal…
When analysing statistical systems or stochastic processes, it is often interesting to ask how they behave given that some observable takes some prescribed value. This conditioning problem is well understood within the linear operator…
The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However, the accuracy and reliability of these methods can vary…
We present a concise derivation of the Boltzmann form for single-particle energy distributions in classical many-body Hamiltonian systems. The derivation relies on two physical facts: coarse-graining-scale invariance of the empirical…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
Obtaining the free energy of large molecules from quantum mechanical energy functions is a longstanding challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the…
We develop Random Batch Methods for interacting particle systems with large number of particles. These methods use small but random batches for particle interactions, thus the computational cost is reduced from $O(N^2)$ per time step to…
We generalize effective energy variational techniques to study appropriately quantized solitonic field configurations. Our approach rests on collective quantization ideas and is specifically designed for the numerical evaluation of soliton…
We examine the performance of several molecular simulation techniques aimed at evaluation of the surface tension through its thermodynamic definition. For all methods explored, the surface tension is calculated by approximating the change…
We go beyond the approximate series-expansions used in the dispersion theory of finite size atoms. We demonstrate that a correct, and non-perturbative, theory dramatically alters the dispersion selfenergies of atoms. The non-perturbed…
Exact free energy minimization is a convex optimization problem that is usually approximated with stochastic sampling methods. Deterministic approximations have been less successful because many desirable properties have been difficult to…